[2024-01-25 19:56:35,689] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:35,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:35,690] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference
[2024-01-25 19:56:36,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:36,778] [INFO] Task started: Prodigal
[2024-01-25 19:56:36,778] [INFO] Running command: gunzip -c /var/lib/cwl/stgce920c4b-fa8b-49bf-9c47-38446963dc13/GCF_014652215.1_ASM1465221v1_genomic.fna.gz | prodigal -d GCF_014652215.1_ASM1465221v1_genomic.fna/cds.fna -a GCF_014652215.1_ASM1465221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:47,111] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:47,111] [INFO] Task started: HMMsearch
[2024-01-25 19:56:47,111] [INFO] Running command: hmmsearch --tblout GCF_014652215.1_ASM1465221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/reference_markers.hmm GCF_014652215.1_ASM1465221v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:47,317] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:47,318] [INFO] Found 6/6 markers.
[2024-01-25 19:56:47,347] [INFO] Query marker FASTA was written to GCF_014652215.1_ASM1465221v1_genomic.fna/markers.fasta
[2024-01-25 19:56:47,347] [INFO] Task started: Blastn
[2024-01-25 19:56:47,347] [INFO] Running command: blastn -query GCF_014652215.1_ASM1465221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/reference_markers.fasta -out GCF_014652215.1_ASM1465221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:48,151] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:48,153] [INFO] Selected 22 target genomes.
[2024-01-25 19:56:48,154] [INFO] Target genome list was writen to GCF_014652215.1_ASM1465221v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:48,171] [INFO] Task started: fastANI
[2024-01-25 19:56:48,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgce920c4b-fa8b-49bf-9c47-38446963dc13/GCF_014652215.1_ASM1465221v1_genomic.fna.gz --refList GCF_014652215.1_ASM1465221v1_genomic.fna/target_genomes.txt --output GCF_014652215.1_ASM1465221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:04,524] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:04,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:04,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:04,540] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:04,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:04,540] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Gemmobacter tilapiae	strain=KCTC 23310	GCA_014652215.1	875041	875041	type	True	100.0	1194	1195	95	conclusive
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.4408	473	1195	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.3249	472	1195	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.1536	414	1195	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.1446	415	1195	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.9497	444	1195	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.9407	427	1195	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	77.8675	430	1195	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	77.8563	416	1195	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.8465	395	1195	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.8208	380	1195	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	77.8077	385	1195	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	77.775	426	1195	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	77.7207	329	1195	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	77.7153	376	1195	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	77.6328	329	1195	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.5428	362	1195	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.5043	330	1195	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.3357	375	1195	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	76.9763	221	1195	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	76.9475	224	1195	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	76.8204	201	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:04,541] [INFO] DFAST Taxonomy check result was written to GCF_014652215.1_ASM1465221v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:04,542] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:04,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:04,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/checkm_data
[2024-01-25 19:57:04,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:04,584] [INFO] Task started: CheckM
[2024-01-25 19:57:04,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652215.1_ASM1465221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652215.1_ASM1465221v1_genomic.fna/checkm_input GCF_014652215.1_ASM1465221v1_genomic.fna/checkm_result
[2024-01-25 19:57:38,887] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:38,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:38,910] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:38,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:38,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652215.1_ASM1465221v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:38,911] [INFO] Task started: Blastn
[2024-01-25 19:57:38,912] [INFO] Running command: blastn -query GCF_014652215.1_ASM1465221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0007519-b1c5-401e-a707-5238c8e4adcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652215.1_ASM1465221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:40,498] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:40,501] [INFO] Selected 24 target genomes.
[2024-01-25 19:57:40,501] [INFO] Target genome list was writen to GCF_014652215.1_ASM1465221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:40,534] [INFO] Task started: fastANI
[2024-01-25 19:57:40,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgce920c4b-fa8b-49bf-9c47-38446963dc13/GCF_014652215.1_ASM1465221v1_genomic.fna.gz --refList GCF_014652215.1_ASM1465221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652215.1_ASM1465221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:58,931] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:58,945] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:58,945] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014652215.1	s__Gemmobacter_C tilapiae	100.0	1194	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008271655.1	s__Gemmobacter caeruleus	78.3245	472	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	78.308	418	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	78.1626	413	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009773375.1	s__Cypionkella sp009773375	78.1112	411	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	78.0831	392	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	78.0711	392	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	77.9798	423	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.9661	375	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	77.949	411	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908315.1	s__Gemmobacter_B sp009908315	77.9419	445	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	77.9302	427	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	77.9269	363	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	77.9072	421	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745575.1	s__ETT8 sp004745575	77.8636	393	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	97.69	97.69	0.90	0.90	2	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	77.8361	398	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973825.1	s__Gemmobacter serpentinus	77.8077	385	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057165.1	s__Tabrizicola sp018057165	77.6857	285	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298485.1	s__JAAFHS01 sp013298485	77.5937	249	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAFHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	77.5118	394	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	77.4279	334	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	77.3319	310	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	77.1704	259	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
GCF_016405985.1	s__Pseudogemmobacter sp016405985	77.1381	284	1195	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:58,947] [INFO] GTDB search result was written to GCF_014652215.1_ASM1465221v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:58,947] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:58,951] [INFO] DFAST_QC result json was written to GCF_014652215.1_ASM1465221v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:58,951] [INFO] DFAST_QC completed!
[2024-01-25 19:57:58,951] [INFO] Total running time: 0h1m23s